scholarly journals Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

2021 ◽  
Vol 22 (9) ◽  
pp. 4745
Author(s):  
Xavier Viader-Godoy ◽  
Maria Manosas ◽  
Felix Ritort
Keyword(s):  
Optical Tweezers ◽  
Conformational Transition ◽  
Persistence Length ◽  
Elastic Response ◽  
Contour Length ◽  
Dna Unwinding ◽  
Chain Model ◽  
Force Extension ◽  
Single Stranded Dna ◽  
Sugar Pucker

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60–14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA.

Characterizing titin's I-band Ig domain region as an entropic spring

1998 ◽  
Vol 111 (11) ◽  
pp. 1567-1574 ◽  
Author(s):  
W.A. Linke ◽  
M.R. Stockmeier ◽  
M. Ivemeyer ◽  
H. Hosser ◽  
P. Mundel
Keyword(s):  
Muscle Protein ◽  
Persistence Length ◽  
Thick Filament ◽  
Contour Length ◽  
Chain Model ◽  
Bending Rigidity ◽  
Force Extension ◽  
Average Force ◽  
Wormlike Chain ◽  
C Terminus

The poly-immunoglobulin domain region of titin, located within the elastic section of this giant muscle protein, determines the extensibility of relaxed myofibrils mainly at shorter physiological lengths. To elucidate this region's contribution to titin elasticity, we measured the elastic properties of the N-terminal I-band Ig region by using immunofluorescence/immunoelectron microscopy and myofibril mechanics and tried to simulate the results with a model of entropic polymer elasticity. Rat psoas myofibrils were stained with titin-specific antibodies flanking the Ig region at the N terminus and C terminus, respectively, to record the extension behaviour of that titin segment. The segment's end-to-end length increased mainly at small stretch, reaching approximately 90% of the native contour length of the Ig region at a sarcomere length of 2.8 microm. At this extension, the average force per single titin molecule, deduced from the steady-state passive length-tension relation of myofibrils, was approximately 5 or 2.5 pN, depending on whether we assumed a number of 3 or 6 titins per half thick filament. When the force-extension curve constructed for the Ig region was simulated by the wormlike chain model, best fits were obtained for a persistence length, a measure of the chain's bending rigidity, of 21 or 42 nm (for 3 or 6 titins/half thick filament), which correctly reproduced the curve for sarcomere lengths up to 3.4 microm. Systematic deviations between data and fits above that length indicated that forces of >30 pN per titin strand may induce unfolding of Ig modules. We conclude that stretches of at least 5–6 Ig domains, perhaps coinciding with known super repeat patterns of these titin modules in the I-band, may represent the unitary lengths of the wormlike chain. The poly-Ig regions might thus act as compliant entropic springs that determine the minute levels of passive tension at low extensions of a muscle fiber.

FINITE ELEMENT MODELING OF THE THERMAL FLUCTUATIONS OF A SINGLE ANISOTROPIC POLYMER

2013 ◽  
Vol 13 (04) ◽  
pp. 1350056
Author(s):  
SANDER L. POELERT ◽  
HARRIE H. WEINANS ◽  
AMIR A. ZADPOOR
Keyword(s):  
Finite Element ◽  
Experimental Work ◽  
Numerical Models ◽  
Persistence Length ◽  
Mean Square Displacement ◽  
Transversely Isotropic ◽  
Thermal Fluctuations ◽  
Contour Length ◽  
Chain Model ◽  
Thermal Dynamics

Thermal fluctuations of microtubules (MTs) and other cytoskeletal filaments govern to a great extent the complex rheological properties of the cytoskeleton in eukaryotic cells. In recent years, much effort has been put into capturing the dynamics of these fluctuations by means of analytical and numerical models. These attempts have been very successful for, but also remain limited to, isotropic polymers. To correctly interpret experimental work on (strongly) anisotropic semiflexible polymers, there is a need for a numerical modeling tool that accurately captures the dynamics of polymers with anisotropic material properties. In the current study, we present a finite element (FE) framework for simulating the thermal dynamics of a single anisotropic semiflexible polymer. First, we demonstrated the accuracy of our framework by comparison of the simulated mean square displacement (MSD) of the end-to-end distance with analytical predictions based on the worm-like chain model. Then, we implemented a transversely isotropic material model, characteristic for biopolymers such as MTs, and studied the persistence length for various ratios between the longitudinal shear modulus, G12, and corresponding Young's modulus, E1. Finally, we put our findings in context by addressing a recent experimental work on grafted transversely isotropic MTs. In that research, a simplified static mechanical model was used to deduce a very high level of MT anisotropy to explain the observation that the persistence length of grafted MTs increases as contour length increases. We showed, by means of our FE framework, that the anisotropic properties cannot account for the reported length-dependent persistence length.

scholarly journals Revealing in real-time a multistep assembly mechanism for SV40 virus-like particles

2020 ◽  
Vol 6 (16) ◽  
pp. eaaz1639 ◽  
Author(s):  
Mariska G. M. van Rosmalen ◽  
Douwe Kamsma ◽  
Andreas S. Biebricher ◽  
Chenglei Li ◽  
Adam Zlotnick ◽  
...  
Keyword(s):  
Real Time ◽  
Optical Tweezers ◽  
Self Assembly ◽  
Persistence Length ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Contour Length ◽  
Sv40 Virus ◽  
Virus Like Particles ◽  
Assembly Mechanism

Many viruses use their genome as template for self-assembly into an infectious particle. However, this reaction remains elusive because of the transient nature of intermediate structures. To elucidate this process, optical tweezers and acoustic force spectroscopy are used to follow viral assembly in real time. Using Simian virus 40 (SV40) virus-like particles as model system, we reveal a multistep assembly mechanism. Initially, binding of VP1 pentamers to DNA leads to a significantly decreased persistence length. Moreover, the pentamers seem able to stabilize DNA loops. Next, formation of interpentamer interactions results in intermediate structures with reduced contour length. These structures stabilize into objects that permanently decrease the contour length to a degree consistent with DNA compaction in wild-type SV40. These data indicate that a multistep mechanism leads to fully assembled cross-linked SV40 particles. SV40 is studied as drug delivery system. Our insights can help optimize packaging of therapeutic agents in these particles.

scholarly journals Semiflexible Polymers Interacting with Planar Surfaces: Weak versus Strong Adsorption

Polymers ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 255 ◽  
Author(s):  
Andrey Milchev ◽  
Kurt Binder
Keyword(s):  
Orientational Order ◽  
Persistence Length ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Gyration Radius ◽  
Contour Length ◽  
Local Order ◽  
Chain Model ◽  
Semiflexible Polymers ◽  
Wide Range

Semiflexible polymers bound to planar substrates by a short-range surface potential are studied by Molecular Dynamics simulations to clarify the extent to which these chain molecules can be considered as strictly two-dimensional. Applying a coarse-grained bead-spring model, the chain length N and stiffness κ as well as the strength of the adsorption potential ϵ w a l l are varied over a wide range. The excluded-volume (EV) interactions inherent in this model can also be “switched off” to provide a discretized version of the Kratky–Porod wormlike chain model. We study both local order parameters (fraction f of monomers within the range of the potential, bond-orientational order parameter η ) and the mean square gyration radius parallel, ⟨ R g 2 ⟩ | | , and perpendicular, ⟨ R g 2 ⟩ ⊥ , to the wall. While for strongly adsorbed chains EV has negligible effect on f and η , we find that ⟨ R g 2 ⟩ | | is strongly affected when the chain contour length exceeds the persistence length. Monomer coordinates in perpendicular (⊥) direction are correlated over the scale of the deflection length which is estimated. It is found that f , η , and ⟨ R g 2 ⟩ ⊥ converge to their asymptotic values with 1 / N corrections. For both weakly and strongly adsorbed chains, the distribution functions of “loops”, “trains”, and “tails” are analyzed. Some consequences pertaining to the analysis of experiments on adsorbed semiflexible polymers are pointed out.

scholarly journals Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers

2019 ◽  
Vol 5 (6) ◽  
pp. eaav1697 ◽  
Author(s):  
Min Ju Shon ◽  
Sang-Hyun Rah ◽  
Tae-Young Yoon
Keyword(s):  
Single Molecule ◽  
Persistence Length ◽  
Gc Content ◽  
Magnetic Tweezers ◽  
Force Variability ◽  
Chain Model ◽  
Force Extension ◽  
Dna Hairpins ◽  
Double Stranded Dna ◽  
Order Of Magnitude

Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.

scholarly journals Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

2018 ◽  
Author(s):  
Debayan Chakraborty ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Electrostatic Interactions ◽  
Persistence Length ◽  
Data Bank ◽  
Coarse Grained ◽  
Force Extension ◽  
Sequence Dependence ◽  
Coarse Grained Model ◽  
Interaction Sites ◽  
Double Stranded Dna ◽  
Centers Of Mass

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

scholarly journals Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sean P. Carney ◽  
Wen Ma ◽  
Kevin D. Whitley ◽  
Haifeng Jia ◽  
Timothy M. Lohman ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Variable Number ◽  
Structural Basis ◽  
Variable Step Size ◽  
Dna Unwinding ◽  
Step Size ◽  
Structural Mechanism ◽  
Dynamics Simulations

AbstractUvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.

scholarly journals Ripping RNA by Force using Gaussian Network Models

2016 ◽  
Author(s):  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Cross Correlation ◽  
Network Models ◽  
Force Extension ◽  
Correlation Matrices ◽  
Rna Molecules ◽  
Allosteric Communication ◽  
Ion Effects ◽  
Gaussian Network

AbstractUsing force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context of proteins have shown that topology plays is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions. Cross-correlation matrices of residue fluctuations, which are analytically calculated using GNM even upon application of mechanical force, show distinct allosteric communication as RNAs rupture. The model is used to calculate the force-extension curves at full thermodynamic equilibrium, and the corresponding unfolding pathways of four RNA molecules subject to a quasi-statically increased force. Our study finds that the analysis using GNM captures qualitatively the unfolding pathway of T. ribozyme elucidated by the optical tweezers measurement. However, the simple model is not sufficient to capture subtle features, such as bifurcation in the unfolding pathways or the ion effects, in the forced-unfolding of RNAs.

scholarly journals DNA and ATP Binding Activities of the Baculovirus DNA Helicase P143

2001 ◽  
Vol 75 (15) ◽  
pp. 7206-7209 ◽  
Author(s):  
Vivien V. McDougal ◽  
Linda A. Guarino
Keyword(s):  
Conformational Change ◽  
Atp Hydrolysis ◽  
Protein Complexes ◽  
Dna Helicase ◽  
Atp Binding ◽  
Dna Unwinding ◽  
Single Stranded Dna ◽  
Inchworm Mechanism

ABSTRACT P143 is a DNA helicase that tightly binds both double-stranded and single-stranded DNA. DNA-protein complexes rapidly dissociated in the presence of ATP and Mg2+. This finding suggests that ATP hydrolysis causes a conformational change in P143 which decreases affinity for DNA. This supports the model of an inchworm mechanism of DNA unwinding.

Sign in / Sign up

Export Citation Format

Share Document